Texture Atlas issues
Check if you have more than one UV Map on the object
If your object already had a UV Map for some reason, TextureAtlas will simply create another UV map. In Blender, per mesh object, at the moment up to 8 different UV maps per mesh are supported. You can see a list of your UV maps in the mesh data tab of your object:

As you can see, by simply clicking at the names, you can switch from one map to the other. The render icon at the right determines which UV map gets passed on to the Texture Coordinates node in the Node Editor:

If the TextureAtlas UV map is all you need, just remove all other maps using the - Button.